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Intro to Data Analysis

Utah Valley University - BIOL3100

Course GitHub Repository

Course Syllabus

Shared Course Notes

(Anyone with link can edit)

The philosophy of this course


Table of Contents

Week 1 | Week 5 | Week 9 | Week 13

Week 2 | Week 6 | Week 10 | Week 14

Week 3 | Week 7 | Week 11 | Week 15

Week 4 | Week 8 | Week 12 | Week 16


The Command Line, File Paths, Git

Week 1

Topics:

  • Installing Software | Command-line | Git version control

Assignments

  • Read: What is Git all about?
  • Install Git, R, and R-Studio on your laptop (part of Assignment 1)
  • Be ready to explain what Git, R, and R-Studio are.
  • Do Assignment 1 and upload a link to your new GitHub account to Canvas.

Resources

Practice

  • Make 10 separate changes and commits to your README.md file and push each one to GitHub

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Week 2

Topics

  • File paths | Pipes | Redirection | Wildcards | Essential Unix Commands | Parameters

Assignments

Resources

Practice

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Getting to Know R

Week 3

Topics

  • R Data types and conversions | Reading and Writing Files | For-Loops | Packages and Projects

Assignments

Resources

Practice

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Week 4

Topics

  • Logical Operations | Subsetting | “Grammar of Graphics” ggplot Intro

Assignments

  • Read through the materials in the Resources section below
  • Assignment 5
  • Exam 1

Resources

Practice

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Visualizing a Data Set

Week 5

Topics

  • ggplot | patchwork | ggforce

Assignments

Resources

Practice

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Clean and Transform Data

Week 6

Topics

  • Tidy Data | dplyr verbs | tidyr verbs

Assignments

Resources

Practice

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Week 7

Topics

Assignments

  • Read This Handout
  • Read This Paper
  • Create a validated Excel Spreadsheet for data collection for the experiment we design in class
  • Exam 2

Resources

Practice

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Getting More From R

Week 8

Topics

  • Writing Functions | Conditional Execution | source()

Assignments

Resources

Practice

  • Write a function that returns the min, max, and mean of any set of real numbers
  • Write a function that takes a data frame and returns a new data frame with one random column removed
  • Write a function that takes a data frame… if there are more than 3 columns, your function should return the column names as-is; if there are 3 or fewer columns, your function should return the column names in reverse order.
  • Write a useful function that you might want to use in the future (your choice)
  • Put all of these functions into a new R script and save it in your main data course repository
  • In a new empty R script, call your functions with source() and test them out

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Model Building and Testing

Week 9

Topics

  • Building and Testing Models

Assignments

Resources

Practice

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Week 10

Topics

  • More models | Statistical Tests

Assignments

Resources

Practice

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Communicating Your Results

Week 11

Topics

  • R-Markdown | Reproducible Reports

Assignments

Resources

Practice

  • Using the resources above, generate a markdown document that analyzes the “iris” data set and push it to a new GitHub repository named Iris_Markdown
  • Play with options and code to create a document that looks good and presents your analysis and results clearly
  • This is similar to Assignment_9, but I’m asking for a brand new “Iris_Markdown” repository that is self-contained.

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Week 12

Topics

  • Proper Project Organization | Collaboration

Assignments

  • Peer evaluation of Assignment 9 (Organization, Portability, Accuracy, Understandablity)
  • Exam 3

Resources

Practice

  • Peer evaluations of Iris_Markdown repositories (from last week); Clean them up and make them more organized

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Putting it all together

Week 13

Topics

  • Data Analysis from raw to report

Assignments

  • We will work together in class to do a complete analysis in real-time

Resources

Practice

  • Analyze the “esoph” data set and generate a markdown report

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Week 14

Topics

  • Building a website with GitHub and R-Markdown

Assignments

  • Work on Final Project
  • Create a GitHub Personal Website
  • Upload a brief CV and the updated (improved) html of Assignment 9 to your new website

Resources

Practice

  • Go through my course website repository (link above) and try to relate the code there to the html version of the website your internet browser is displays

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Week 15

Topics

  • TBD

Assignments

  • Work on Final Project

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Week 16

Topics

  • TBD

Assignments

  • Exam 4 (Redo any previous exam to replace it’s score)

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